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17
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4
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8.9k
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Tutorial:
Updated Support Site Editor
support.bioconductor.org
editor
markdown
updates
Tutorial
updated 24 days ago by
Mj.A.
• 0 • written 5.2 years ago by
shepherl
3.8k
14
votes
21
replies
1.7k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
updated 6 hours ago by
Robert Castelo
★ 3.2k • written 21 days ago by
Chris
• 0
11
votes
5
replies
7.3k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 1 day ago by
Garrett
• 0 • written 9.1 years ago by
brohawndg
▴ 150
10
votes
10
replies
6.4k
views
biomaRt not working - lazy table error
error
lazy
R
biomaRt
table
updated 29 days ago by
juo5
• 0 • written 5 months ago by
Abhishek
▴ 10
9
votes
12
replies
7.7k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 1 day ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
8
votes
23
replies
793
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 8 days ago by
Robert Castelo
★ 3.2k • written 9 days ago by
Bine
▴ 40
7
votes
36
replies
5.5k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 16 days ago by
Shiva
• 0 • written 5.4 years ago by
Guido Hooiveld
★ 3.9k
7
votes
6
replies
414
views
Batch Effect Correction, Gene Filtering
DGE
limma
updated 28 days ago by
Gordon Smyth
50k • written 28 days ago by
Amit
• 0
6
votes
10
replies
1.5k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 1 day ago by
i.atanasoai
• 0 • written 14 months ago by
mohammedtoufiq91
▴ 10
6
votes
10
replies
2.2k
views
overlapsAny for elements in GRangesList
granges
grangeslist
overlapsAny
updated 6 days ago by
Samuel Ahuno
• 0 • written 8.0 years ago by
maltethodberg
▴ 170
6
votes
5
replies
383
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC
minifi
written 7 weeks ago by
Kim
• 0
5
votes
3
replies
670
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR
DifferentialExpression
updated 23 days ago by
Gordon Smyth
50k • written 4 weeks ago by
Jack S.
▴ 50
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 2 days ago by
Gordon Smyth
50k • written 6 months ago by
Jonathan
▴ 10
5
votes
7
replies
419
views
DEG Filtering
MicroarrayData
limma
Genefiltering
updated 23 days ago by
Gordon Smyth
50k • written 4 weeks ago by
Amit
• 0
5
votes
9
replies
811
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
9 days ago • updated 2 days ago
Chris
• 0
5
votes
14
replies
2.2k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 22 hours ago by
Seyram M.
• 0 • written 4.6 years ago by
hsbio
▴ 10
5
votes
25
replies
795
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 15 days ago by
Gordon Smyth
50k • written 25 days ago by
Jitendra
▴ 10
5
votes
6
replies
384
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 7 days ago by
ATpoint
★ 4.0k • written 10 days ago by
nhaus
▴ 30
4
votes
16
replies
7.3k
views
Normalised counts from RUVg in RUVSeq
RUVg
ruvseq
rnaseq
updated 29 days ago by
Shaimaa Gamal
• 0 • written 8.9 years ago by
Pauly Lin
▴ 150
4
votes
8
replies
308
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 1 day ago by
Peter Hickey
▴ 740 • written 9 days ago by
Juan Higareda
• 0
3
votes
5
replies
327
views
Differing results from plotMDS and PCAtools
edgeR
PCAtools
updated 20 days ago by
Gordon Smyth
50k • written 22 days ago by
Fabian
• 0
3
votes
2
replies
191
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2
Transcriptomics
25 days ago
Anita
▴ 10
3
votes
3
replies
337
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater
runPCA
updated 25 days ago by
alan.ocallaghan
▴ 160 • written 26 days ago by
Najla Abassi
• 0
3
votes
1
reply
1.4k
views
Job:
Post Doctoral position in AI (Deep learning / Machine learning) approaches for Cancer Research, MRC Cancer Unit, University of Cambridge, UK
job
Job
machine learning
deep learning
computational biology
written 6.3 years ago by
Shamith.Samarajiwa
▴ 180
3
votes
3
replies
145
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
8 days ago • updated 2 days ago
jacques.imbert
• 0
3
votes
3
replies
267
views
permutation test in edgeR
rna-seq
edgeR
updated 5 days ago by
Gordon Smyth
50k • written 12 days ago by
Netanel
• 0
3
votes
6
replies
217
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
9 days ago • updated 8 days ago
nhaus
▴ 30
3
votes
1
reply
734
views
News:
[Pre-print] Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex
biorxiv
spatialLIBD
News
written 4.1 years ago by
Leonardo Collado Torres
★ 1.0k
3
votes
3
replies
13k
views
How to fix 'long vectors not supported yet' error in R
r
updated 16 days ago by
Amruta
• 0 • written 5.2 years ago by
r.tor
• 0
3
votes
18
replies
2.8k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
9 months ago • updated 2 days ago
shepherl
3.8k
2
votes
1
reply
211
views
Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran
bluster
scater
scuttle
updated 26 days ago by
ATpoint
★ 4.0k • written 26 days ago by
Dario Strbenac
★ 1.5k
2
votes
3
replies
227
views
Rsubread crashes Rstudio while alignment
Rsubjunc
Rsubread
updated 25 days ago by
Wei Shi
★ 3.6k • written 25 days ago by
thomas.heigl.ibk
• 0
2
votes
2
replies
139
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
8 days ago • updated 5 days ago
daniel.carbajo
• 0
2
votes
5
replies
996
views
STRINGdb R package reference class instantiation with v12.0
STRINGdb
updated 15 days ago by
damian.szk
▴ 80 • written 5 months ago by
Abhishek
• 0
2
votes
2
replies
139
views
[DiffBind] Obtaining normalization factors
DiffBind
7 days ago • updated 4 days ago
Henry
▴ 10
2
votes
1
reply
180
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
updated 26 days ago by
Guido Hooiveld
★ 3.9k • written 28 days ago by
enee
▴ 10
2
votes
2
replies
152
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
7 days ago
julia_mcdonough
• 0
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 3 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
2
votes
3
replies
266
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
5 days ago • updated 4 days ago
daniel.carbajo
• 0
2
votes
2
replies
194
views
From a DNAStringSet to a data.frame
Biostrings
25 days ago • updated 24 days ago
ramiro.barrantes
▴ 10
2
votes
2
replies
159
views
Bluster and Varieties of Louvain Clulstering
bluster
updated 15 days ago by
ATpoint
★ 4.0k • written 15 days ago by
Dario Strbenac
★ 1.5k
2
votes
6
replies
313
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
11 days ago
Chris
• 0
2
votes
6
replies
437
views
limma: vooma mean-variance trend and data filtration
MicroarrayData
limma
6 weeks ago • updated 25 days ago
Lily Cheang
▴ 10
2
votes
8
replies
478
views
Microarray Limma Model fitting and DEG
limma
DGEanalysis
updated 23 days ago by
Gordon Smyth
50k • written 24 days ago by
Amit
• 0
2
votes
3
replies
317
views
PCA of different bacterial species
DESeq2
updated 24 days ago by
Michael Love
41k • written 24 days ago by
Laura
▴ 10
2
votes
6
replies
1.3k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP
DMRcate
minfi
updated 17 days ago by
Tim Peters
▴ 170 • written 4 months ago by
rae.alshammari
▴ 10
2
votes
5
replies
708
views
Looking for equivalent EPIC chip v1 vs. v2 annotation variables
sesame
IlluminaHumanMethylationEPICv2anno.20a1.hg38
methylationEPICv2.0
EpicV2
updated 29 days ago by
aldea85
• 0 • written 5 months ago by
Courtney
• 0
2
votes
2
replies
1.6k
views
Running featureCounts() in 'IntersectionStrict' mode
rsubread
featurecounts
summarizeoverlaps
updated 19 days ago by
isaac.vock
• 0 • written 7.8 years ago by
Jon Manning
▴ 90
2
votes
2
replies
344
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
8 days ago • updated 7 days ago
Henry
▴ 10
2
votes
5
replies
672
views
DESeq2 setting significant p-value
DESeq2
updated 23 hours ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
203 results • Page
1 of 5
Recent ...
Replies
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Robert Castelo
★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq
by
lonn
• 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph
by
deeenes
▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches
by
Gordon Smyth
50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param
by
russ.bainer
▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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